<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
    <title>Learning the Tools</title>
    <meta content="text/html; charset=iso-8859-1"
          http-equiv="Content-Type">
</head>
<body>
<table bgcolor="maroon" border="1" width="99%">
    <tbody>
    <tr>
        <td>
            <h2><font color="white">Tetrad Toolbar </font></h2>
        </td>
    </tr>
    </tbody>
</table>
<p>The main toolbar allows you select box types to place in the main workspace
    (the white area). It also allows you to select tools for selecting and moving
    boxes and for drawing arrows between them. Each button in the toolbar is explained below. <br>
</p>

<h3>Select and Move Button </h3>
<img height="43" src="../images/select_move_button.gif" width="113"><br>
<p> When the movement button is highlighted,&nbsp; the objects in the
    workspace can be moved around by
    clicking over each nodes and dragging it elsewhere in the workspace. </p>
<p>Once you have created a box, its contents can be opened by double clicking
    on it. The contents may be another workbench for creating an nodes, or may
    be the nodes itself once it has been created:</p>
<p>The button at the bottom left of the toolbar column--the one with a
    red and a green arrow--permits you to make a flow chart connecting
    boxes you have placed in the workspace. <br>
</p>

<h3>Flow Chart Button</h3>
<p><img height="44" src="../images/arrow_button.gif" width="114"><br>
    <br>
    To make a flow chart, simply click on the flow chart tool button, and then click
    on the box you want at the tail of a flowchart arrow and drag the arrow to the
    box you want at the head of the flow chart arrow. You can do this repeatedly
    without having to click on the .flow chart tool button in between. Only one
    flowchart arrow can connect any two boxes, but a box can have any number of
    flowchart arrows out of it.</p>
<p><img height="90" src="../images/graph1_to_pm1.gif" width="244"></p>
<p>The flow chart you create provides the input to each Tetrad operation. Some
    boxes require no input (e.g, the Graph boz), some require one input (e..g.,
    PM box requires a Graph box as input) and some boxes require several inputs
    (e.g., th Estimate box requires&nbsp; a Data box and a PM box.). Not all connections
    are allowed, and if you attempt to connect two boxes that cannot be related
    (e.g., two graph boxes), the flowchart tool will simple refuse to make the connecting
    arrow.<br>
    <br>
    If you put the cursor over a box and let it rest for a moment, a "tip" appears
    that describes the inputs required for the operations in that box. <br>
</p>

<h2>The Tool Buttons </h2>
<p>Each tool button when clicked allows the creation of a corresponding box inside
    the workspace. Various operations can be carried out by opening a box, provided
    it has appropriate inputs. The results of the operations are contained in, and
    remain accessible inside of the box in whcih they are created. Running an operation
    or program inside a box never creates a new box. We will describe each of the
    other tool buttons and how to use them for a variety of tasks. <span style="font-style: italic;">Clicking
  in this file on the tool buttons illustrated below will provide much more information 
  about each of their functions and operation.</span><br>
</p>

<h3>Data & Simulation</h3>
<p><img height="43" src="../images/data_button.gif" width="113"></p>
<p>Creates a Data & Similation box which can be used to load data from a file, or create
    simulated data, or manipulate one data set to create another one
    and allows the importation of data files from outside the
    program..<br>
</p>

<h3>Search</h3>
<p><img height="43" src="../images/search_button.gif" width="113"></p>
<p><font size="+1"><span style="font-weight: bold;">Search Button</span></font></p>
<p>Creates a Search box, which allows one to perform a search algorithm on
    specified data to produce a graph. Please see the help items for the
    Search box for details, as many algorithms are available for use. The
    idea is, one put a Data & Simulation box on the workbench (see above),
    then puts a Search box on the workbench, then uses the Flowchart
    Tool to draw an edge from the Data & Simulation box to the Search
    box. One then double clicks the Data & Simulatio box and either
    loads data or creates a simulation and closes this box. Then one
    double clicks the Search box, selects a search algorithm using the
    pull-down menus, and clicks Search. The result appears in a new
    tab.<br>
</p>

<h3>Knowledge</h3>
<p><img height="43" src="../images/knowledge_button.png" width="113"></p>
<p>Creates a Knowledge box, which allows one to specify background
    knowledge for a search. Note that the knowledge editor for
    Tiers & Edges is included in the search box for algorithms that
    can use it. However, other types of knowledge can ben specified,
    and in some cases one wants to use the same knowledge for more
    than one search. In these cases, the Knowledge box is helpful.
    <br>
</p>

<h3>Compare Model</h3>
<p><img height="44" src="../images/compare_button.gif" width="114"><br>
</p>
<p>Creates a Comparison box. The Comparison box allows one to perform
    various types of comparisons between two boxes. Many of the comparisons
    take a Search and a Graph as inputs and produce a comparisons of the
    edges between the two boxes. These can be used to judge how accurate
    the search results are compared to a true DAG, or the CPDAG or PAG
    of the true DAG.
    <br>
</p>

<h3>Graph Model</h3>
</p><img height="45" src="../images/graph_button.gif" width="114"></p>
<p>Creates a Graph box. Options are:</p>
<ul>
    <li><i>DAG (Directed Acyclic Graph)</i> - Produces a graph consisting
        entirely of directed edges, where no cycles are formed--that is,
        where there is no path X1->X1->...X1 of a variable back to
        itself.<br>
    </li>
    <li><i>General Graph</i> - A set of variables over which a set of
        edges has been defined, where the edges can be of any of the four
        standard Tetrad edge types. Cycles can be created in this type of
        graph<br>
    </li>
    <li><i>Lag Graph</i> - A set of variables, each at a series of time
        lags. Directed edges may extend from previous time lags into the
        current time step. The time series graph is interpreted as a repeating
        update graph.
    </li>
</ul>

<h3>Parametric Model</h3>
<p><img height="43" src="../images/pm_button.gif" width="113"></p>
<p>Creates a PM box in which a parametric model can be created. A
    parametric model specifies the family of probability
    functions connecting cause and effect,a, but does
    NOT specify values for its parameters.For example, if you open the PM
    box a dialog box will come up giving simple alternatives. One
    alternative, for example, is "Bayes net." If you choose that, the graph
    you have specified as input to the PM box will be parametrized as a
    categorical model in which the parameters are the (unspecified)
    conditional probabilities of values of each variable on the values
    of&nbsp; its parent variables in the graph. If you specify "SEM," the
    graph will be parametrized as a linear Gaussian model, with variances
    and linear coefficients. The values for the parameters in the
    parametric model selected are NOT in PM. They must be specified in an
    IM box, which must have a flowchart arrow from a PM box directed into
    it.<br>
</p>

<h3>Instantiated Model </h3>
<p><img height="44" src="../images/im_button.gif" width="114"></p>
<p>Creates an IM box, which can be used to create an instantiated
    model. An instantiated model specifies particular numberical values
    for the parameters of a parametric model. Arbitrary parameter values
    are entered randomly and can be edited in a window created from the IM
    box<br>
</p>

<h3>Estimator Button</h3>
<p><img height="44" src="../images/estimator_button.gif" width="113"></p>
<p>Creates an Estimator box. Given a PM and Data, the procedures in the
    statistical estimator allow estimation of the parameters--that is,
    creation of an instantiated model, based on the Data input to the
    Estimator box.&nbsp; Estimators include maximum liklelihood and
    Dirichlet types. There are also procedures <br>
    for handling missing values.</p>

<h3>Updater Button</h3>
<p><img height="44" src="../images/updater_button.gif" width="113"></p>
<p>Creates an Update box. The Update box requires input from an IM box that is a Bayes net--i.e., is for discrete
    variables. It will compute the conditional probability of any variable in the Bayes net given values for any other
    variables in the model. It will also compute such probabilities condiitonal on an <span style="font-style: italic;">intervention </span>the
    fixes or randomizes other variables. </p>

<h3>Classify Button</h3>
<p><img height="45" src="../images/classify_button.gif" width="114"></p>
<p>Classify creates a Classifier box, which requires input from Data and from an IM box. It is used to classify new
    cases with the Bayes net in the IM box.. The variables in the IM box must match some of the variables in the Data.
    The user specifies a target variable in the IM and the classifier uses the Bayes net structure of the IM to predict
    the values of the target&nbsp; in the data set. Statistics on classification accuracy are provided (as ROC curves
    and confusion matrices.) </p>
<h3>Regression Button</h3>

<p><img height="45" src="../images/regression_button.gif" width="114"></p>
<p>Creates a Regression box, which allows the user to perform multiple linear regressions
    or logistic regressions.</p>
</body>
</html>
